ArticleDNA research : an international journal for rapid publication of reports on genes and genomes2014
Solution hybrid selection capture for the recovery of functional full-length eukaryotic cDNAs from complex environmental samples.
Article in DNA research : an international journal for rapid publication of reports on genes and genomes, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers.
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Who cites it
13 citing papers in PubMed.
- Probe Capture Enrichment Sequencing of amoA Genes Improves the Detection of Diverse Ammonia-Oxidising Archaeal and Bacterial Populations.Molecular ecology resources · 2025Article
- Metagenomics and metatranscriptomics as potential driving forces for the exploration of diversity and functions of micro-eukaryotes in soil.3 Biotech · 2023Review
- Fungal dye-decolorizing peroxidase diversity: roles in either intra- or extracellular processes.Applied microbiology and biotechnology · 2022Article
- Screening New Xylanase Biocatalysts from the Mangrove Soil Diversity.Microorganisms · 2021Article
- Exploring the Diversity of Fungal DyPs in Mangrove Soils to Produce and Characterize Novel Biocatalysts.Journal of fungi (Basel, Switzerland) · 2021Article
- ORF Capture-Seq as a versatile method for targeted identification of full-length isoforms.Nature communications · 2020Article
- Metatranscriptomics: an approach for retrieving novel eukaryotic genes from polluted and related environments.3 Biotech · 2020Review
- Effective mosquito and arbovirus surveillance using metabarcoding.Molecular ecology resources · 2018Article
- The sequence capture by hybridization: a new approach for revealing the potential of mono-aromatic hydrocarbons bioattenuation in a deep oligotrophic aquifer.Microbial biotechnology · 2017Article
- OCaPPI-Db: an oligonucleotide probe database for pathogen identification through hybridization capture.Database : the journal of biological databases and curation · 2017Article
- Sequence capture by hybridization to explore modern and ancient genomic diversity in model and nonmodel organisms.Nucleic acids research · 2016Review
- Environmental microbiology as a mosaic of explored ecosystems and issues.Environmental science and pollution research international · 2015Review
- Discovery of new protein families and functions: new challenges in functional metagenomics for biotechnologies and microbial ecology.Frontiers in microbiology · 2015Review
Corrections and comments
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Authors and funding
10 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Eukaryotic microbial communities play key functional roles in soil biology and potentially represent a rich source of natural products including biocatalysts. Culture-independent molecular methods are powerful tools to isolate functional genes from uncultured microorganisms. However, none of the methods used in environmental genomics allow for a rapid isolation of numerous functional genes from eukaryotic microbial communities. We developed an original adaptation of the solution hybrid selection (SHS) for an efficient recovery of functional complementary DNAs (cDNAs) synthesized from soil-extracted polyadenylated mRNAs. This protocol was tested on the Glycoside Hydrolase 11 gene family encoding endo-xylanases for which we designed 35 explorative 31-mers capture probes. SHS was implemented on four soil eukaryotic cDNA pools. After two successive rounds of capture, >90% of the resulting cDNAs were GH11 sequences, of which 70% (38 among 53 sequenced genes) were full length. Between 1.5 and 25% of the cloned captured sequences were expressed in Saccharomyces cerevisiae. Sequencing of polymerase chain reaction-amplified GH11 gene fragments from the captured sequences highlighted hundreds of phylogenetically diverse sequences that were not yet described, in public databases. This protocol offers the possibility of performing exhaustive exploration of eukaryotic gene families within microbial communities thriving in any type of environment.
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